ImageJ Macros

Recording macros is a simple way to automate repetitive tasks.

Some great courses are provided by the IJ developers community ( for ex. at the EMBL-CMCI by Kota Miura). Other resources can be found on the IJ website or FIJI WIKI.

Reusable snippets of code for general tasks can be found on the FIJI WIKI here

Macros are provided here as .txt files. To get them working in (FI)IJ follow: open (file>new>script> file>open [*.txt] then set language> imagej macro.

Run to get started…